The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: IDUA vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000203.5(IDUA):c.300-3C>G

CA549265042

551563 (ClinVar)

Gene: IDUA
Condition: mucopolysaccharidosis type 1
Inheritance Mode: Autosomal recessive inheritance
UUID: ff706fd6-7a8f-4363-9f62-177e4ef29003
Approved on: 2025-05-23
Published on: 2025-05-23

HGVS expressions

NM_000203.5:c.300-3C>G
NM_000203.5(IDUA):c.300-3C>G
NC_000004.12:g.1000609C>G
CM000666.2:g.1000609C>G
NC_000004.11:g.994397C>G
CM000666.1:g.994397C>G
NC_000004.10:g.984397C>G
NG_008103.1:g.18613C>G
ENST00000247933.9:c.300-3C>G
ENST00000514224.2:c.300-3C>G
ENST00000652070.1:n.356-3C>G
ENST00000247933.8:c.300-3C>G
ENST00000502910.5:c.159-3C>G
ENST00000504568.5:c.260-3C>G
ENST00000506561.5:n.309-3C>G
ENST00000508168.5:n.178-3C>G
ENST00000509948.5:c.93-3C>G
ENST00000514192.5:c.117-3C>G
ENST00000514224.1:c.-97-3C>G
ENST00000514698.5:n.200-3C>G
NM_000203.4:c.300-3C>G
NR_110313.1:n.388-3C>G
NM_001363576.1:c.-97-3C>G
More

Pathogenic

Met criteria codes 3
PM2_Supporting PP4_Moderate PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Lysosomal Diseases Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for IDUA Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000203.5:c.300-3C>G variant in IDUA occurs within the splice acceptor region of intron 2. RT-PCR of fibroblast RNA from an individual who is compound heterozygous for the variant (labeled as 388-3C>G in the publication) revealed that the variant results in insertion of 58 intronic nucleotides, which would result in a frameshift). Analysis of heterozygous polymorphic markers showed that the variant caused a significant decrease in the level of IDUA mRNA derived from the allele with the c.300-3C>G variant. Furthermore, expression of the variant in COS-7 cells resulted in 1.6% wild type IDUA activity with no IDUA protein detected on western blot (PMID: 10735634) (PVS1). Two patients with this variant had documented IDUA deficiency within the affected range in leukocytes, urinary GAGs above the normal range, or clinical features specific to MPS I including hepatosplenomegaly, corneal involvement, skeletal and cardiac abnormalities (PMID: 10735634, 29801497). (PP4_Moderate). These individuals are compound heterozygous for the variant and another variant in IDUA, c.1037T>G or c.1874A>C) (PMID: 10735634, 29801497). The allelic data from these patients will be used in the classification of the second variant and is not included here to avoid circular logic (PM3 not applied). The highest population minor allele frequency in gnomAD v4.1.0 is 0.00004557 (2/44876 alleles) in the EAS population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting). In summary, this variant meets the criteria to be classified as Pathogenic for MPS I based on the IDUA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert panel (Specifications Version 1.0.0): PVS1, PP4_Moderate, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on May 23, 2025)
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0 is 0.00004557 (2/44876 alleles) in the EAS population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).
PP4_Moderate
At least two patients with this variant had documented IDUA deficiency within the affected range in leukocytes, urinary GAGs above the normal range, or clinical features specific to MPS I including hepatosplenomegaly, corneal involvement, skeletal and cardiac abnormalities (PMID: 10735634, 29801497) (PP4_Moderate)
PVS1
The NM_000203.5:c.300-3C>G variant in IDUA occurs within the splice acceptor region of intron 2. RT-PCR of fibroblast RNA from an individual who is compound heterozygous for the variant (labeled as 388-3C>G in the publication) revealed that the variant results in insertion of 58 intronic nucleotides, which would result in a frameshift). Furthermore, analysis of heterozygous polymorphic markers showed that the variant caused a significant decrease in the level of IDUA mRNA derived from the allele with the c.300-3C>G variant (PMID: 10735634) (PVS1).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.